Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168159.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_4, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 33012953
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 65000 characters in sequence are not A, C, G, or T
File 15 of 160
Found at i:4451389 original size:28 final size:27
Alignment explanation
Indices: 4451350--4451413 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 27
4451340 GATTGAGAGA
4451350 ATATAT-A-TAAGTTTATACCAATATG
1 ATATATAAGTAAGTTTATACCAATATG
* **
4451375 ATGTTATAAGTAAGTTTATATGAATATG
1 AT-ATATAAGTAAGTTTATACCAATATG
4451403 ATATATAAGTA
1 ATATATAAGTA
4451414 CAAATAATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
25 2 0.06
26 3 0.09
27 9 0.28
28 18 0.56
ACGTcount: A:0.44, C:0.03, G:0.12, T:0.41
Consensus pattern (27 bp):
ATATATAAGTAAGTTTATACCAATATG
Found at i:4457021 original size:22 final size:22
Alignment explanation
Indices: 4456995--4457038 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
4456985 TGTATATTTA
*
4456995 TATTTGTATCTCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
4457017 TATTTGTATCCCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
4457039 GACAAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (22 bp):
TATTTGTATCCCTAGAATTAAG
Found at i:4457224 original size:25 final size:25
Alignment explanation
Indices: 4457181--4457230 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
4457171 AATATACATT
4457181 CAGTTTTTCTCTTAA-TTTTTCACA
1 CAGTTTTTCTCTTAATTTTTTCACA
* *
4457205 CAGTTTTATTTCTTAGTTTTTTCACA
1 CAGTTTT-TCTCTTAATTTTTTCACA
4457231 TGGTATCAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 7 0.32
25 6 0.27
26 9 0.41
ACGTcount: A:0.20, C:0.18, G:0.06, T:0.56
Consensus pattern (25 bp):
CAGTTTTTCTCTTAATTTTTTCACA
Found at i:4457329 original size:25 final size:25
Alignment explanation
Indices: 4457295--4457354 Score: 120
Period size: 25 Copynumber: 2.4 Consensus size: 25
4457285 TGACTTCTAT
4457295 TTTAGGCCTTCATTGCCGAACCCTG
1 TTTAGGCCTTCATTGCCGAACCCTG
4457320 TTTAGGCCTTCATTGCCGAACCCTG
1 TTTAGGCCTTCATTGCCGAACCCTG
4457345 TTTAGGCCTT
1 TTTAGGCCTT
4457355 TATAGCCATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.15, C:0.30, G:0.20, T:0.35
Consensus pattern (25 bp):
TTTAGGCCTTCATTGCCGAACCCTG
Found at i:4461080 original size:22 final size:22
Alignment explanation
Indices: 4461054--4461097 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
4461044 TGTATATTTA
4461054 TATTTGTA-TCTCTAGAATTAAG
1 TATTTGTATTC-CTAGAATTAAG
4461076 TATTTGTATTCCTAGAATTAAG
1 TATTTGTATTCCTAGAATTAAG
4461098 GACAATAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 19 0.90
23 2 0.10
ACGTcount: A:0.32, C:0.09, G:0.14, T:0.45
Consensus pattern (22 bp):
TATTTGTATTCCTAGAATTAAG
Found at i:4461283 original size:25 final size:25
Alignment explanation
Indices: 4461240--4461289 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
4461230 AATATACATT
4461240 CAGTTTTTATCTTAA-TTTTTCACA
1 CAGTTTTTATCTTAATTTTTTCACA
* *
4461264 CAGTTTTATTTCTTAGTTTTTTCACA
1 CAGTTTT-TATCTTAATTTTTTCACA
4461290 ATAGTAACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 7 0.32
25 6 0.27
26 9 0.41
ACGTcount: A:0.22, C:0.16, G:0.06, T:0.56
Consensus pattern (25 bp):
CAGTTTTTATCTTAATTTTTTCACA
Found at i:4468238 original size:19 final size:19
Alignment explanation
Indices: 4468216--4468267 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
4468206 AAATTAAATA
4468216 ATTAAATAATAA-ATATAAT
1 ATTAAAT-ATAATATATAAT
*
4468235 ATTAAATATAATATTTAAT
1 ATTAAATATAATATATAAT
* *
4468254 TTTAAATTTAATAT
1 ATTAAATATAATAT
4468268 GATATTTAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 4 0.14
19 25 0.86
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
ATTAAATATAATATATAAT
Found at i:4468240 original size:12 final size:12
Alignment explanation
Indices: 4468220--4468249 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
4468210 TAAATAATTA
*
4468220 AATAATAAATAT
1 AATATTAAATAT
4468232 AATATTAAATAT
1 AATATTAAATAT
4468244 AATATT
1 AATATT
4468250 TAATTTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
AATATTAAATAT
Found at i:4468274 original size:12 final size:12
Alignment explanation
Indices: 4468227--4468276 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
4468217 TTAAATAATA
*
4468227 AATATAATATTA
1 AATATAATATTT
4468239 AATATAATATTT
1 AATATAATATTT
*
4468251 AATTTTAA-ATTT
1 AA-TATAATATTT
*
4468263 AATATGATATTT
1 AATATAATATTT
4468275 AA
1 AA
4468277 CTTAAAAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
11 3 0.09
12 25 0.78
13 4 0.12
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (12 bp):
AATATAATATTT
Found at i:4468375 original size:27 final size:29
Alignment explanation
Indices: 4468345--4468440 Score: 91
Period size: 29 Copynumber: 3.5 Consensus size: 29
4468335 CACATGAATA
4468345 AATAATATTTTAAATTT-TATATTA-ATT
1 AATAATATTTTAAATTTATATATTATATT
*
4468372 AAT-ATA-TTTATAATTTATATATTATGTT
1 AATAATATTTTA-AATTTATATATTATATT
*
4468400 AA-AAT-TTTTAAAAATTTAAATATTATATT
1 AATAATATTTT--AAATTTATATATTATATT
4468429 AA-AA-ATTTTAAA
1 AATAATATTTTAAA
4468441 AATTAAAAAT
Statistics
Matches: 58, Mismatches: 3, Indels: 16
0.75 0.04 0.21
Matches are distributed among these distances:
25 4 0.07
26 8 0.14
27 13 0.22
28 9 0.16
29 23 0.40
30 1 0.02
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (29 bp):
AATAATATTTTAAATTTATATATTATATT
Found at i:4468422 original size:29 final size:29
Alignment explanation
Indices: 4468383--4468444 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
4468373 ATATATTTAT
* * *
4468383 AATTTATATATTATGTTAAAATTTTTAAA
1 AATTTAAATATTATATTAAAAATTTTAAA
4468412 AATTTAAATATTATATTAAAAATTTTAAA
1 AATTTAAATATTATATTAAAAATTTTAAA
4468441 AATT
1 AATT
4468445 AAAAATAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (29 bp):
AATTTAAATATTATATTAAAAATTTTAAA
Found at i:4468438 original size:21 final size:20
Alignment explanation
Indices: 4468407--4468445 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
4468397 GTTAAAATTT
*
4468407 TTAAAAATTTAAATATTATA
1 TTAAAAATTTAAAAATTATA
4468427 TTAAAAATTTTAAAAATTA
1 TTAAAAA-TTTAAAAATTA
4468446 AAAATAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TTAAAAATTTAAAAATTATA
Found at i:4468460 original size:29 final size:29
Alignment explanation
Indices: 4468399--4468462 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
4468389 TATATTATGT
* * * *
4468399 TAAAATTTTTAAAAATTTAAATATTATAT
1 TAAAAATTTTAAAAATTAAAATATAATAA
4468428 TAAAAATTTTAAAAATTAAAA-ATAAATAA
1 TAAAAATTTTAAAAATTAAAATAT-AATAA
4468457 TAAAAA
1 TAAAAA
4468463 ATGAAAAGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 2 0.07
29 28 0.93
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (29 bp):
TAAAAATTTTAAAAATTAAAATATAATAA
Found at i:4468462 original size:21 final size:22
Alignment explanation
Indices: 4468438--4468479 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
4468428 TAAAAATTTT
*
4468438 AAAAATTAAAAAT-AAATAATA
1 AAAAATGAAAAATAAAATAATA
*
4468459 AAAAATGAAAAGTAAAATAAT
1 AAAAATGAAAAATAAAATAAT
4468480 CTAGTAACAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (22 bp):
AAAAATGAAAAATAAAATAATA
Found at i:4469772 original size:79 final size:81
Alignment explanation
Indices: 4469641--4469802 Score: 274
Period size: 79 Copynumber: 2.0 Consensus size: 81
4469631 TTTGGCCTTG
4469641 GGGATCTTGGGGGAGAGGAGTGTTGATGGCATGTTTGCACACACGCCAATATATGTA-TGTG-TG
1 GGGATCTTGGGGGAGAGGAGTGTTGATGGCATGTTTGCACACACGCCAATATATGTAGTGTGATG
4469704 TACAATACATCCACAT
66 TACAATACATCCACAT
* *
4469720 GGGATCTTGGGGGAGAGGAGTGTTGATGGCATGTTTGCACACATGCCCATATATGTATGTGTGTA
1 GGGATCTTGGGGGAGAGGAGTGTTGATGGCATGTTTGCACACACGCCAATATATGTA-GTGTG-A
4469785 TGTACAATACATCCACAT
64 TGTACAATACATCCACAT
4469803 TTTTAGGAAG
Statistics
Matches: 77, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
79 55 0.71
81 4 0.05
83 18 0.23
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (81 bp):
GGGATCTTGGGGGAGAGGAGTGTTGATGGCATGTTTGCACACACGCCAATATATGTAGTGTGATG
TACAATACATCCACAT
Found at i:4472217 original size:30 final size:28
Alignment explanation
Indices: 4472161--4472219 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
4472151 GGAGAGCGCG
4472161 AAAGCTTCGTGTACAAGAATTATAAAAA
1 AAAGCTTCGTGTACAAGAATTATAAAAA
* * * *
4472189 AAAGGTTCGTGTGCAAGAATTGTATAAA
1 AAAGCTTCGTGTACAAGAATTATAAAAA
4472217 AAA
1 AAA
4472220 TGAAAAATGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.47, C:0.08, G:0.19, T:0.25
Consensus pattern (28 bp):
AAAGCTTCGTGTACAAGAATTATAAAAA
Found at i:4473966 original size:133 final size:131
Alignment explanation
Indices: 4473706--4473980 Score: 444
Period size: 131 Copynumber: 2.1 Consensus size: 131
4473696 TGGGAATTTG
* * *
4473706 TCTGTTTGCTGTTGATGAAGCACACTGCATATCTGAATGGGGCCATGATTTCAGGTCATTGATGC
1 TCTGGTTGCTGTTGATGAAACACACTGCATATCTGAATGGGGCCATGATTTCAGGTCACTGATGC
* * *
4473771 TATTTTTTTTCCCTTAATACTTCATTTTTCATATTTCCACTGAGCATGCTATTCCTATTTCCTTT
66 TATTTTTTTTCCCTTAATACTTCATTATTCATATTTCCACTGAGCATACTATTCCTAGTTCCTTT
4473836 T
131 T
* *
4473837 TGTGGTTGCTGTTGATGAAACACATTGCATATCTGAATGGGGCCATGATTTCAGGTCACTGATGC
1 TCTGGTTGCTGTTGATGAAACACACTGCATATCTGAATGGGGCCATGATTTCAGGTCACTGATGC
*
4473902 TATTTATTTTTCCCCTTAATACTTCATTATTGATATTTCCACTGAGCATACTATTCCTAGTTCCT
66 TATTT-TTTTT-CCCTTAATACTTCATTATTCATATTTCCACTGAGCATACTATTCCTAGTTCCT
4473967 TTT
129 TTT
4473970 TCTGGTT-CTGT
1 TCTGGTTGCTGT
4473981 GGGGACAAAT
Statistics
Matches: 132, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
131 65 0.49
132 9 0.07
133 58 0.44
ACGTcount: A:0.20, C:0.20, G:0.16, T:0.43
Consensus pattern (131 bp):
TCTGGTTGCTGTTGATGAAACACACTGCATATCTGAATGGGGCCATGATTTCAGGTCACTGATGC
TATTTTTTTTCCCTTAATACTTCATTATTCATATTTCCACTGAGCATACTATTCCTAGTTCCTTT
T
Found at i:4482542 original size:32 final size:31
Alignment explanation
Indices: 4482506--4482602 Score: 73
Period size: 32 Copynumber: 3.2 Consensus size: 31
4482496 TATGGTATTT
4482506 AGAAAGAAAGATTTGTATAGGCTTATGTAAAG
1 AGAAAGAAAGATTTGTATAGGCTTATGT-AAG
* *
4482538 AGAAAAATTAAGTGATTT-TAT-GG--TAT-T--T
1 AGAAAGA--AA--GATTTGTATAGGCTTATGTAAG
4482566 AGAAAGAAAGATTTGTATAGGCTTATGTACAG
1 AGAAAGAAAGATTTGTATAGGCTTATGTA-AG
4482598 AGAAA
1 AGAAA
4482603 AATTAACTTG
Statistics
Matches: 49, Mismatches: 4, Indels: 24
0.64 0.05 0.31
Matches are distributed among these distances:
24 5 0.10
25 3 0.06
26 4 0.08
28 9 0.18
29 1 0.02
31 1 0.02
32 14 0.29
34 4 0.08
35 3 0.06
36 5 0.10
ACGTcount: A:0.43, C:0.03, G:0.23, T:0.31
Consensus pattern (31 bp):
AGAAAGAAAGATTTGTATAGGCTTATGTAAG
Found at i:4482580 original size:60 final size:60
Alignment explanation
Indices: 4482487--4482608 Score: 235
Period size: 60 Copynumber: 2.0 Consensus size: 60
4482477 GTAACCTTGA
4482487 AAGTGATTTTATGGTATTTAGAAAGAAAGATTTGTATAGGCTTATGTAAAGAGAAAAATT
1 AAGTGATTTTATGGTATTTAGAAAGAAAGATTTGTATAGGCTTATGTAAAGAGAAAAATT
*
4482547 AAGTGATTTTATGGTATTTAGAAAGAAAGATTTGTATAGGCTTATGTACAGAGAAAAATT
1 AAGTGATTTTATGGTATTTAGAAAGAAAGATTTGTATAGGCTTATGTAAAGAGAAAAATT
4482607 AA
1 AA
4482609 CTTGCTGAAG
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 61 1.00
ACGTcount: A:0.42, C:0.02, G:0.21, T:0.34
Consensus pattern (60 bp):
AAGTGATTTTATGGTATTTAGAAAGAAAGATTTGTATAGGCTTATGTAAAGAGAAAAATT
Found at i:4486522 original size:14 final size:15
Alignment explanation
Indices: 4486498--4486541 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
4486488 TATCAATTAA
4486498 ATTTAAATATAATTT
1 ATTTAAATATAATTT
4486513 ATTT-AATATAATTT
1 ATTTAAATATAATTT
* *
4486527 TTTTCAATCATAATT
1 ATTTAAAT-ATAATT
4486542 ATAATAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 13 0.50
15 7 0.27
16 6 0.23
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.55
Consensus pattern (15 bp):
ATTTAAATATAATTT
Found at i:4488463 original size:17 final size:17
Alignment explanation
Indices: 4488443--4488481 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
4488433 TTATTTTTTA
4488443 TTTTA-ATTTTTAGAATT
1 TTTTATATTTTTA-AATT
*
4488460 TTTTATATTTTTATATT
1 TTTTATATTTTTAAATT
4488477 TTTTA
1 TTTTA
4488482 GAAAATTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.72
Consensus pattern (17 bp):
TTTTATATTTTTAAATT
Found at i:4488490 original size:27 final size:27
Alignment explanation
Indices: 4488426--4488504 Score: 79
Period size: 27 Copynumber: 2.8 Consensus size: 27
4488416 TTATTTAATC
* *
4488426 AAAATATTTATTTTTTATTTTAATTTTTAG
1 AAAAT-TTTATTTTTTA--ATATTTTTTAG
**
4488456 AATTTTTTATATTTTT-ATATTTTTTAG
1 AAAATTTTAT-TTTTTAATATTTTTTAG
4488483 AAAATTTTATTTTTTAATATTT
1 AAAATTTTATTTTTTAATATTT
4488505 AAATAAAAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
26 5 0.12
27 23 0.56
29 5 0.12
30 8 0.20
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (27 bp):
AAAATTTTATTTTTTAATATTTTTTAG
Found at i:4490115 original size:13 final size:12
Alignment explanation
Indices: 4490093--4490125 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
4490083 TACGGACATA
4490093 ATAA-TTTTTTT
1 ATAATTTTTTTT
4490104 ATAAATTTTTTTT
1 AT-AATTTTTTTT
4490117 ATAATTTTT
1 ATAATTTTT
4490126 AATTCAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 2 0.10
12 9 0.45
13 9 0.45
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
ATAATTTTTTTT
Found at i:4491659 original size:10 final size:9
Alignment explanation
Indices: 4491642--4491716 Score: 57
Period size: 9 Copynumber: 8.0 Consensus size: 9
4491632 CGTTTTTAAA
4491642 TTTTT-TTT
1 TTTTTATTT
*
4491650 TTTTCATTT
1 TTTTTATTT
4491659 TTTTTATTT
1 TTTTTATTT
4491668 GTTTTTAACTCTGT
1 -TTTTT-A-T-T-T
4491682 TTTTT-TTT
1 TTTTTATTT
4491690 TTTTT-TTT
1 TTTTTATTT
*
4491698 TTTTTTTTT
1 TTTTTATTT
4491707 TTTTCTATTT
1 TTTT-TATTT
4491717 GTTTATTGAT
Statistics
Matches: 56, Mismatches: 3, Indels: 14
0.77 0.04 0.19
Matches are distributed among these distances:
8 18 0.32
9 19 0.34
10 10 0.18
11 1 0.02
12 1 0.02
13 6 0.11
14 1 0.02
ACGTcount: A:0.07, C:0.05, G:0.03, T:0.85
Consensus pattern (9 bp):
TTTTTATTT
Found at i:4491685 original size:1 final size:1
Alignment explanation
Indices: 4491681--4491710 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
4491671 TTTAACTCTG
4491681 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
4491711 CTATTTGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:4510452 original size:45 final size:46
Alignment explanation
Indices: 4510388--4510478 Score: 166
Period size: 46 Copynumber: 2.0 Consensus size: 46
4510378 GATCTAAGGA
4510388 CAGAAGAAGGATAACTG-AAATTAAGTCACAATGTGTTGCTAAATG
1 CAGAAGAAGGATAACTGAAAATTAAGTCACAATGTGTTGCTAAATG
*
4510433 CAGAAGAAGGATAACTGAAAATTAAGTCATAATGTGTTGCTAAATG
1 CAGAAGAAGGATAACTGAAAATTAAGTCACAATGTGTTGCTAAATG
4510479 TTGATATGAA
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
45 17 0.39
46 27 0.61
ACGTcount: A:0.43, C:0.10, G:0.22, T:0.25
Consensus pattern (46 bp):
CAGAAGAAGGATAACTGAAAATTAAGTCACAATGTGTTGCTAAATG
Found at i:4517173 original size:5 final size:5
Alignment explanation
Indices: 4517163--4517187 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
4517153 CTGTTGTCTC
4517163 CTTTT CTTTT CTTTT CTTTT CTTTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT
4517188 TGACCTTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
CTTTT
Found at i:4524099 original size:18 final size:18
Alignment explanation
Indices: 4524063--4524100 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
4524053 CATCTCTGGT
*
4524063 TGTTGTTGCTGATGCTGC
1 TGTTGTTGCTGATGATGC
4524081 TGTTGTTGCTG-TAGATGC
1 TGTTGTTGCTGAT-GATGC
4524099 TG
1 TG
4524101 CTGGTGCTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 1 0.06
18 17 0.94
ACGTcount: A:0.08, C:0.13, G:0.34, T:0.45
Consensus pattern (18 bp):
TGTTGTTGCTGATGATGC
Found at i:4526233 original size:19 final size:19
Alignment explanation
Indices: 4526211--4526253 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
4526201 AAGGATGGGT
4526211 AAAAAGAA-AAAGAG-TATA
1 AAAAAGAATAAAG-GTTATA
4526229 AAAAAGAATAAAGGTTATA
1 AAAAAGAATAAAGGTTATA
4526248 AAAAAG
1 AAAAAG
4526254 GGGTTGGTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 9 0.39
19 14 0.61
ACGTcount: A:0.70, C:0.00, G:0.16, T:0.14
Consensus pattern (19 bp):
AAAAAGAATAAAGGTTATA
Found at i:4526344 original size:2 final size:2
Alignment explanation
Indices: 4526337--4526372 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
4526327 GGCCCTTGGG
4526337 GA GA GA GA GA GA G- GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
4526373 TATCTTATTG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
GA
Found at i:4534110 original size:17 final size:18
Alignment explanation
Indices: 4534083--4534119 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
4534073 ATTTTGAATA
4534083 ATTTTTATATTATTAA-TT
1 ATTTTTATATT-TTAAGTT
4534101 ATTTTT-TATTTTAAGTT
1 ATTTTTATATTTTAAGTT
4534118 AT
1 AT
4534120 ATAAATTTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 4 0.22
17 8 0.44
18 6 0.33
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (18 bp):
ATTTTTATATTTTAAGTT
Found at i:4534150 original size:16 final size:15
Alignment explanation
Indices: 4534131--4534164 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
4534121 TAAATTTACC
*
4534131 TATTCATAAATATAAT
1 TATTCACAAATAT-AT
4534147 TATTCACAAATATAT
1 TATTCACAAATATAT
4534162 TAT
1 TAT
4534165 ATTTATTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (15 bp):
TATTCACAAATATAT
Found at i:4551851 original size:6 final size:6
Alignment explanation
Indices: 4551840--4551886 Score: 62
Period size: 6 Copynumber: 8.2 Consensus size: 6
4551830 GAGTCACCAC
* *
4551840 TCTTTT TCTTTT TCTTTT T-TTTT ACTTAT TCTTTT TCTTTT T-TTTT
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT
4551886 T
1 T
4551887 ACTTAGAGAT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
5 9 0.25
6 27 0.75
ACGTcount: A:0.04, C:0.13, G:0.00, T:0.83
Consensus pattern (6 bp):
TCTTTT
Found at i:4551871 original size:17 final size:16
Alignment explanation
Indices: 4551842--4551880 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
4551832 GTCACCACTC
*
4551842 TTTTTCTTTTTCTTTT
1 TTTTTCTTATTCTTTT
4551858 TTTTTACTTATTCTTTT
1 TTTTT-CTTATTCTTTT
4551875 TCTTTT
1 T-TTTT
4551881 TTTTTTACTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 5 0.25
17 11 0.55
18 4 0.20
ACGTcount: A:0.05, C:0.13, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTTTCTTATTCTTTT
Found at i:4551875 original size:23 final size:24
Alignment explanation
Indices: 4551845--4551891 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
4551835 ACCACTCTTT
4551845 TTCTTTTTC-TTTTTTTTTACTTA
1 TTCTTTTTCTTTTTTTTTTACTTA
4551868 TTCTTTTTCTTTTTTTTTTACTTA
1 TTCTTTTTCTTTTTTTTTTACTTA
4551892 GAGATAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 9 0.39
24 14 0.61
ACGTcount: A:0.09, C:0.13, G:0.00, T:0.79
Consensus pattern (24 bp):
TTCTTTTTCTTTTTTTTTTACTTA
Found at i:4552523 original size:45 final size:44
Alignment explanation
Indices: 4552450--4552537 Score: 106
Period size: 45 Copynumber: 2.0 Consensus size: 44
4552440 TTTTATTTTT
* *
4552450 ATTTTTTATTTCAAATTTTTCATCATTTGAATCAATTTAGAAAA
1 ATTTTTTATTTCAAAATTTTCATCATTTGAAGCAATTTAGAAAA
* * *
4552494 ATTTTTTATTTTTAAAATTTTCA-CTATTTGGAGCTATTTAGAAA
1 ATTTTTTA-TTTCAAAATTTTCATC-ATTTGAAGCAATTTAGAAA
4552538 TTCTCTCTCT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
44 9 0.24
45 28 0.76
ACGTcount: A:0.34, C:0.08, G:0.07, T:0.51
Consensus pattern (44 bp):
ATTTTTTATTTCAAAATTTTCATCATTTGAAGCAATTTAGAAAA
Found at i:4554335 original size:19 final size:21
Alignment explanation
Indices: 4554313--4554355 Score: 54
Period size: 19 Copynumber: 2.1 Consensus size: 21
4554303 TAATTTTTTT
*
4554313 ATTTTAAAAAT-AT-ATTAAA
1 ATTTGAAAAATAATCATTAAA
*
4554332 ATTTGAAGAATAATCATTAAA
1 ATTTGAAAAATAATCATTAAA
4554353 ATT
1 ATT
4554356 AAGATTTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 9 0.45
20 2 0.10
21 9 0.45
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (21 bp):
ATTTGAAAAATAATCATTAAA
Found at i:4554571 original size:14 final size:14
Alignment explanation
Indices: 4554552--4554593 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
4554542 TTGTTATTAA
4554552 TAATATAATAATAT
1 TAATATAATAATAT
4554566 TAATATAATAATAT
1 TAATATAATAATAT
*
4554580 TTAT-TAAT-ATAT
1 TAATATAATAATAT
4554592 TA
1 TA
4554594 TTTATAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
12 5 0.19
13 4 0.15
14 17 0.65
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TAATATAATAATAT
Found at i:4554597 original size:15 final size:15
Alignment explanation
Indices: 4554563--4554699 Score: 55
Period size: 15 Copynumber: 8.5 Consensus size: 15
4554553 AATATAATAA
4554563 TATTAATATAATAATATT
1 TATTAATAT-AT--TATT
4554581 TATTAATATATTATT
1 TATTAATATATTATT
*
4554596 TA-TAA-ATAGTATT
1 TATTAATATATTATT
* * *
4554609 TAATTATTATATGAAT
1 T-ATTAATATATTATT
* *
4554625 AAATAATATATTATT
1 TATTAATATATTATT
* *
4554640 AATATAAAAAATAATAATATT
1 --TAT---TAAT-ATATTATT
*
4554661 TATAAATATATT-TCT
1 TATTAATATATTAT-T
*
4554676 TATTAATATAATATT
1 TATTAATATATTATT
4554691 TATATAATA
1 TAT-TAATA
4554700 AAATAATTAT
Statistics
Matches: 90, Mismatches: 17, Indels: 26
0.68 0.13 0.20
Matches are distributed among these distances:
13 8 0.09
14 5 0.06
15 37 0.41
16 15 0.17
17 3 0.03
18 9 0.10
19 3 0.03
20 3 0.03
21 7 0.08
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (15 bp):
TATTAATATATTATT
Found at i:4554619 original size:29 final size:29
Alignment explanation
Indices: 4554563--4554699 Score: 96
Period size: 26 Copynumber: 4.9 Consensus size: 29
4554553 AATATAATAA
4554563 TATTAATATAATAATATTTATTAATATAT
1 TATTAATATAATAATATTTATTAATATAT
* *
4554592 TATTTATA-AATAGTATTTAATT-AT-TA-
1 TATTAATATAATAATATTT-ATTAATATAT
*
4554618 TATGAATA-AATAATATATTATTAATATA-
1 TATTAATATAATAATAT-TTATTAATATAT
* *
4554646 -A--AAAATAATAATATTTATAAATATATT
1 TATTAATATAATAATATTTATTAATATA-T
* *
4554673 TCTTATTA-ATATAATATTTATATAATA
1 TATTAATATA-ATAATATTTAT-TAATA
4554700 AAATAATTAT
Statistics
Matches: 85, Mismatches: 11, Indels: 22
0.72 0.09 0.19
Matches are distributed among these distances:
25 13 0.15
26 24 0.28
27 7 0.08
28 13 0.15
29 11 0.13
30 13 0.15
31 4 0.05
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (29 bp):
TATTAATATAATAATATTTATTAATATAT
Found at i:4554640 original size:23 final size:24
Alignment explanation
Indices: 4554611--4554670 Score: 70
Period size: 23 Copynumber: 2.5 Consensus size: 24
4554601 ATAGTATTTA
*
4554611 ATTATT-ATATGAATAAATAAT-AT
1 ATTATTAATAT-AAAAAATAATAAT
4554634 ATTATTAATATAAAAAATAATAAT
1 ATTATTAATATAAAAAATAATAAT
*
4554658 ATTTATAAATATA
1 A-TTATTAATATA
4554671 TTTCTTATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
23 15 0.47
24 7 0.22
25 10 0.31
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (24 bp):
ATTATTAATATAAAAAATAATAAT
Found at i:4561407 original size:20 final size:22
Alignment explanation
Indices: 4561340--4561422 Score: 62
Period size: 23 Copynumber: 3.7 Consensus size: 22
4561330 AGTTTTATAA
* **
4561340 TAAAATATATATATATTAAAATT
1 TAAAAT-TATAAATATTATTATT
*
4561363 TAAAATTATTAAATATTATTTTT
1 TAAAATTA-TAAATATTATTATT
*
4561386 TAAAATTA-AAATTTTA-TATT
1 TAAAATTATAAATATTATTATT
*
4561406 TAATACATTATTAATAT
1 TAA-A-ATTATAAATAT
4561423 ATAAATTTTA
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
20 6 0.12
21 8 0.17
22 6 0.12
23 28 0.58
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (22 bp):
TAAAATTATAAATATTATTATT
Found at i:4561570 original size:23 final size:24
Alignment explanation
Indices: 4561540--4561585 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
4561530 TATTTGATTC
*
4561540 ATTGATAATATA-TAAATTTAAAT
1 ATTGATAATATATTAAATATAAAT
*
4561563 ATTGATAATGTATTAAATATAAA
1 ATTGATAATATATTAAATATAAA
4561586 CTCTAAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (24 bp):
ATTGATAATATATTAAATATAAAT
Found at i:4562256 original size:20 final size:20
Alignment explanation
Indices: 4562231--4562272 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
4562221 TTCTATTTTA
* *
4562231 AGGTTCATTTATATTTATTT
1 AGGTTCATTTACACTTATTT
*
4562251 AGGTTCGTTTACACTTATTT
1 AGGTTCATTTACACTTATTT
4562271 AG
1 AG
4562273 CATTTGTTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.24, C:0.10, G:0.14, T:0.52
Consensus pattern (20 bp):
AGGTTCATTTACACTTATTT
Found at i:4562880 original size:25 final size:25
Alignment explanation
Indices: 4562823--4562880 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
4562813 TTTTTTTAAA
4562823 ATGAAATATTAAAAAATCCCAAAAAT
1 ATGAAA-ATTAAAAAATCCCAAAAAT
* * * *
4562849 CTAAAAATTAAAAAATCCGAAACAT
1 ATGAAAATTAAAAAATCCCAAAAAT
4562874 ATGAAAA
1 ATGAAAA
4562881 ATTCAAATAT
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
25 22 0.85
26 4 0.15
ACGTcount: A:0.62, C:0.12, G:0.05, T:0.21
Consensus pattern (25 bp):
ATGAAAATTAAAAAATCCCAAAAAT
Found at i:4563076 original size:11 final size:11
Alignment explanation
Indices: 4563060--4563084 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
4563050 CTTTTCTAAG
4563060 TTTTTGTGAAT
1 TTTTTGTGAAT
4563071 TTTTTGTGAAT
1 TTTTTGTGAAT
4563082 TTT
1 TTT
4563085 ATGAAAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.16, T:0.68
Consensus pattern (11 bp):
TTTTTGTGAAT
Found at i:4563173 original size:18 final size:19
Alignment explanation
Indices: 4563152--4563189 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
4563142 TTTTAATTAC
*
4563152 TTTAATTTTTCAT-AATTT
1 TTTAATTTTTAATAAATTT
*
4563170 TTTATTTTTTAATAAATTT
1 TTTAATTTTTAATAAATTT
4563189 T
1 T
4563190 AAAAAATGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTAATTTTTAATAAATTT
Found at i:4563392 original size:25 final size:25
Alignment explanation
Indices: 4563335--4563394 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
4563325 TATTTTTAAA
4563335 ATGAAATATTAAAAAATCCCAAAAAT
1 ATGAAA-ATTAAAAAATCCCAAAAAT
* *
4563361 CTAAAAATTAAAAAAT-CCAAAATAT
1 ATGAAAATTAAAAAATCCCAAAA-AT
4563386 ATGAAAATT
1 ATGAAAATT
4563395 TCAAATATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 6 0.21
25 19 0.66
26 4 0.14
ACGTcount: A:0.62, C:0.10, G:0.03, T:0.25
Consensus pattern (25 bp):
ATGAAAATTAAAAAATCCCAAAAAT
Found at i:4564501 original size:2 final size:2
Alignment explanation
Indices: 4564494--4564528 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
4564484 GGTTGAATTT
* *
4564494 TG TG TG TG TG TG TG TG TG TG TT TG TG TG AG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
4564529 TTTCTTTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.03, C:0.00, G:0.46, T:0.51
Consensus pattern (2 bp):
TG
Found at i:4570961 original size:2 final size:2
Alignment explanation
Indices: 4570954--4570979 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4570944 CATCACCTCC
4570954 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
4570980 ATTCTAATAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4571676 original size:19 final size:20
Alignment explanation
Indices: 4571637--4571680 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
4571627 AATTAATCAA
*
4571637 AAATAAAAATTTTTATTATT
1 AAATAAAAATTTATATTATT
*
4571657 AAATAAAGATTTAT-TTATT
1 AAATAAAAATTTATATTATT
4571676 AAATA
1 AAATA
4571681 TATAATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (20 bp):
AAATAAAAATTTATATTATT
Found at i:4572185 original size:21 final size:21
Alignment explanation
Indices: 4572144--4572183 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
4572134 AATTTTAGAT
*
4572144 TATTATTTTTATATCTATTTA
1 TATTAATTTTATATCTATTTA
4572165 TATTAATTTTATATC-ATTT
1 TATTAATTTTATATCTATTT
4572184 TAACACTATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (21 bp):
TATTAATTTTATATCTATTTA
Found at i:4573226 original size:29 final size:26
Alignment explanation
Indices: 4573190--4573242 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 26
4573180 TAATAAGTAA
*
4573190 ATTTTTTTAAAAATATTAATTTTTATAT
1 ATTTTTTT--AAATATTAATATTTATAT
4573218 ATTTATTTTAAATATTAATATTTAT
1 ATTT-TTTTAAATATTAATATTTAT
4573243 TCGTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 15 0.65
28 4 0.17
29 4 0.17
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (26 bp):
ATTTTTTTAAATATTAATATTTATAT
Found at i:4573239 original size:15 final size:15
Alignment explanation
Indices: 4573200--4573240 Score: 52
Period size: 13 Copynumber: 2.9 Consensus size: 15
4573190 ATTTTTTTAA
4573200 AAATATTAAT-TTTT
1 AAATATTAATATTTT
*
4573214 ATATATT--TATTTT
1 AAATATTAATATTTT
4573227 AAATATTAATATTT
1 AAATATTAATATTT
4573241 ATTCGTTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
12 1 0.05
13 10 0.45
14 6 0.27
15 5 0.23
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
AAATATTAATATTTT
Found at i:4576019 original size:2 final size:2
Alignment explanation
Indices: 4576009--4576046 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
4575999 ATTTTTTAAA
4576009 AG AG A- AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
4576047 AAAGGGTCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4578622 original size:12 final size:11
Alignment explanation
Indices: 4578596--4578632 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
4578586 TATTTTTTTG
*
4578596 ATTTTATTA-A
1 ATTTTTTTATA
4578606 ATTTTTTTATA
1 ATTTTTTTATA
4578617 ATTTTTTTATA
1 ATTTTTTTATA
4578628 ATTTT
1 ATTTT
4578633 AAACTAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
10 8 0.32
11 17 0.68
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
ATTTTTTTATA
Found at i:4590219 original size:21 final size:21
Alignment explanation
Indices: 4590186--4590234 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
4590176 AAACAAAAGA
* *
4590186 AAGAGGATAATGATAATGAAG
1 AAGAAGATAATGAAAATGAAG
*
4590207 AAGAAGATGATGAAAATGAAG
1 AAGAAGATAATGAAAATGAAG
*
4590228 ATGAAGA
1 AAGAAGA
4590235 AGATAACAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.55, C:0.00, G:0.29, T:0.16
Consensus pattern (21 bp):
AAGAAGATAATGAAAATGAAG
Found at i:4610513 original size:12 final size:11
Alignment explanation
Indices: 4610467--4610516 Score: 59
Period size: 10 Copynumber: 4.6 Consensus size: 11
4610457 CGTAGGTGAG
4610467 AAATTTT-TAA
1 AAATTTTATAA
4610477 AAATTTTATAA
1 AAATTTTATAA
* *
4610488 ACATATTA-AA
1 AAATTTTATAA
4610498 AAATTTATATAA
1 AAATTT-TATAA
4610510 AAATTTT
1 AAATTTT
4610517 TTATATCAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
10 13 0.39
11 12 0.36
12 8 0.24
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (11 bp):
AAATTTTATAA
Found at i:4616853 original size:14 final size:15
Alignment explanation
Indices: 4616836--4616865 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4616826 TTTTAAACCA
4616836 ATTTAAA-TAAATTT
1 ATTTAAATTAAATTT
4616850 ATTTAAATTAAATTT
1 ATTTAAATTAAATTT
4616865 A
1 A
4616866 GTACATTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTTAAATTAAATTT
Found at i:4617024 original size:20 final size:19
Alignment explanation
Indices: 4616985--4617026 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
4616975 AAAAATATCC
* *
4616985 TTAAATTATTTTTCTTTTT
1 TTAAATTATTTTTATATTT
4617004 TTAAATATATTTTTATATTT
1 TTAAAT-TATTTTTATATTT
4617024 TTA
1 TTA
4617027 TTATATTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (19 bp):
TTAAATTATTTTTATATTT
Found at i:4617129 original size:23 final size:23
Alignment explanation
Indices: 4617102--4617157 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
4617092 AATTATTTAT
*
4617102 ATTAAAAATTTATTTAGATATAA
1 ATTAAAAATTTATTTAAATATAA
**
4617125 ATTAAAAGCTTATTTAAATATAA
1 ATTAAAAATTTATTTAAATATAA
4617148 ATTAAAAATT
1 ATTAAAAATT
4617158 AAAAATTTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.41
Consensus pattern (23 bp):
ATTAAAAATTTATTTAAATATAA
Found at i:4617158 original size:30 final size:29
Alignment explanation
Indices: 4617123--4617251 Score: 100
Period size: 30 Copynumber: 4.3 Consensus size: 29
4617113 ATTTAGATAT
*
4617123 AAATTAAAAGCTTATTTAAATATAAATTAA
1 AAATTAAAAGTTTATTTAAATATAAA-TAA
* ** *
4617153 AAATTAAAAATTTATTTGGATGTAAATAA
1 AAATTAAAAGTTTATTTAAATATAAATAA
* * *
4617182 AAGATTAGAAGTTTATTTGAATGT-AATAA
1 AA-ATTAAAAGTTTATTTAAATATAAATAA
* * *
4617211 AAATATAAAAATTTATCTAAATA-AAATTGTA
1 AAAT-TAAAAGTTTATTTAAATATAAA-T-AA
4617242 AAATTAAAAG
1 AAATTAAAAG
4617252 GCTCTTTTAT
Statistics
Matches: 79, Mismatches: 15, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
28 2 0.03
29 27 0.34
30 45 0.57
31 5 0.06
ACGTcount: A:0.54, C:0.02, G:0.09, T:0.36
Consensus pattern (29 bp):
AAATTAAAAGTTTATTTAAATATAAATAA
Found at i:4617209 original size:29 final size:29
Alignment explanation
Indices: 4617123--4617226 Score: 111
Period size: 30 Copynumber: 3.5 Consensus size: 29
4617113 ATTTAGATAT
** * *
4617123 AAATTAAAAGCTTATTTAAATATAAATTAA
1 AAATTAAAAATTTATTTGAATGTAAA-TAA
*
4617153 AAATTAAAAATTTATTTGGATGTAAATAA
1 AAATTAAAAATTTATTTGAATGTAAATAA
* *
4617182 AAGATTAGAAGTTTATTTGAATGT-AATAA
1 AA-ATTAAAAATTTATTTGAATGTAAATAA
4617211 AAATATAAAAATTTAT
1 AAAT-TAAAAATTTAT
4617227 CTAAATAAAA
Statistics
Matches: 62, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
28 2 0.03
29 21 0.34
30 39 0.63
ACGTcount: A:0.53, C:0.01, G:0.09, T:0.38
Consensus pattern (29 bp):
AAATTAAAAATTTATTTGAATGTAAATAA
Found at i:4625151 original size:22 final size:19
Alignment explanation
Indices: 4625121--4625170 Score: 55
Period size: 22 Copynumber: 2.5 Consensus size: 19
4625111 TTCCATCAAT
*
4625121 TAAATTAATTATTAAAATTAAA
1 TAAAATAATTATT--AATT-AA
*
4625143 TAAAATAATTATTTATTAA
1 TAAAATAATTATTAATTAA
4625162 TAAAATAAT
1 TAAAATAAT
4625171 ATCATTGACC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 11 0.42
20 3 0.12
22 12 0.46
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
TAAAATAATTATTAATTAA
Found at i:4628652 original size:11 final size:11
Alignment explanation
Indices: 4628636--4628676 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
4628626 CGACTTGGAG
4628636 AGAAAAAAAAA
1 AGAAAAAAAAA
4628647 AGAAAAAAAAA
1 AGAAAAAAAAA
* **
4628658 AGGAAGGAAAA
1 AGAAAAAAAAA
4628669 AGAAAAAA
1 AGAAAAAA
4628677 GGAGAAGAAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (11 bp):
AGAAAAAAAAA
Found at i:4628694 original size:18 final size:17
Alignment explanation
Indices: 4628646--4628699 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 17
4628636 AGAAAAAAAA
*
4628646 AAGAAAAAAAAAAGGAAGG
1 AAGAAAGAAAAAAGG-A-G
4628665 AA-AAAGAAAAAAGGAG
1 AAGAAAGAAAAAAGGAG
*
4628681 AAGAAAGAACAAAAAGAG
1 AAGAAAGAA-AAAAGGAG
4628699 A
1 A
4628700 GGAGAAGCTC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
16 3 0.10
17 7 0.23
18 19 0.61
19 2 0.06
ACGTcount: A:0.74, C:0.02, G:0.24, T:0.00
Consensus pattern (17 bp):
AAGAAAGAAAAAAGGAG
Found at i:4632029 original size:30 final size:30
Alignment explanation
Indices: 4631985--4632064 Score: 90
Period size: 30 Copynumber: 2.6 Consensus size: 30
4631975 AACTGAACGC
*
4631985 TCAATTGAGGTGAAAATAAATGTTAAAAAGT
1 TCAATT-ATGTGAAAATAAATGTTAAAAAGT
* * *
4632016 TCAATTATGTGAAAATAGATGTTTAAAGGT
1 TCAATTATGTGAAAATAAATGTTAAAAAGT
*
4632046 TCAATTTAT-TCAAAATAAA
1 TCAA-TTATGTGAAAATAAA
4632065 AAAAATTAAG
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
30 32 0.76
31 10 0.24
ACGTcount: A:0.46, C:0.05, G:0.15, T:0.34
Consensus pattern (30 bp):
TCAATTATGTGAAAATAAATGTTAAAAAGT
Found at i:4634321 original size:4 final size:4
Alignment explanation
Indices: 4634312--4634344 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
4634302 AGATTGTTGT
4634312 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA T
1 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA T
4634345 AATAATAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TTAA
Found at i:4634349 original size:3 final size:3
Alignment explanation
Indices: 4634341--4634371 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
4634331 ATTAATTAAT
4634341 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
4634372 CCTTTTGACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:4636513 original size:2 final size:2
Alignment explanation
Indices: 4636506--4636552 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
4636496 GATGATGGGT
4636506 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
4636548 GA TA T
1 TA TA T
4636553 CTTGATGTTC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:4642946 original size:21 final size:22
Alignment explanation
Indices: 4642916--4642967 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
4642906 GATATTTTTA
4642916 AATA-TTTATA-TTTAAAAAAT
1 AATATTTTATATTTTAAAAAAT
4642936 AATATTTTATATTTTAAAAAAT
1 AATATTTTATATTTTAAAAAAT
4642958 AATATTTTAT
1 AATATTTTAT
4642968 TAATTTCGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 4 0.13
21 6 0.20
22 20 0.67
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
AATATTTTATATTTTAAAAAAT
Found at i:4649353 original size:2 final size:2
Alignment explanation
Indices: 4649348--4649374 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4649338 GCAGCGGGGG
4649348 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
4649375 CAAGAGACAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:4651708 original size:10 final size:11
Alignment explanation
Indices: 4651683--4651712 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
4651673 TTTTAAATTT
4651683 TATTATTTTAA
1 TATTATTTTAA
4651694 TATTATTTT-A
1 TATTATTTTAA
4651704 TATTATTTT
1 TATTATTTT
4651713 TATGTCATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
TATTATTTTAA
Found at i:4651713 original size:11 final size:11
Alignment explanation
Indices: 4651683--4651715 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
4651673 TTTTAAATTT
*
4651683 TATTATTTTAA
1 TATTATTTTTA
4651694 TATTA-TTTTA
1 TATTATTTTTA
4651704 TATTATTTTTA
1 TATTATTTTTA
4651715 T
1 T
4651716 GTCATATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
TATTATTTTTA
Found at i:4653220 original size:21 final size:22
Alignment explanation
Indices: 4653172--4653221 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
4653162 TAATATTATT
* *
4653172 TAATTTAATCTTATTCATAACA
1 TAATTTTATCTTAGTCATAACA
* *
4653194 TTATTTTATCTT-GTCATATCA
1 TAATTTTATCTTAGTCATAACA
4653215 TAATTTT
1 TAATTTT
4653222 GTGTATCAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.32, C:0.12, G:0.02, T:0.54
Consensus pattern (22 bp):
TAATTTTATCTTAGTCATAACA
Found at i:4653862 original size:15 final size:15
Alignment explanation
Indices: 4653842--4653882 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
4653832 TTTATTTAAT
4653842 TTATATTAATATATA
1 TTATATTAATATATA
4653857 TTATATTAATA-A-A
1 TTATATTAATATATA
4653870 TTAT-TTAATATAT
1 TTATATTAATATAT
4653883 TAATTTAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 6 0.25
13 6 0.25
14 1 0.04
15 11 0.46
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TTATATTAATATATA
Found at i:4653888 original size:13 final size:12
Alignment explanation
Indices: 4653833--4653897 Score: 60
Period size: 13 Copynumber: 5.2 Consensus size: 12
4653823 ATTTTATTGT
*
4653833 TTATTTAATTTA
1 TTATTTAATATA
*
4653845 -TATTAATATATA
1 TTATTTA-ATATA
*
4653857 TTATATTAATAAA
1 TTAT-TTAATATA
4653870 TTATTTAATATA
1 TTATTTAATATA
*
4653882 TTAATTTAAAATA
1 TT-ATTTAATATA
4653895 TTA
1 TTA
4653898 ACTTAATAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
11 5 0.12
12 14 0.33
13 22 0.51
14 2 0.05
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
TTATTTAATATA
Found at i:4658292 original size:20 final size:21
Alignment explanation
Indices: 4658254--4658292 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
4658244 CTTTTCCACT
**
4658254 TTATTATTCCTTTTTCTTTTC
1 TTATTATTCCTTTCCCTTTTC
4658275 TTATT-TTCCTTTCCCTTT
1 TTATTATTCCTTTCCCTTT
4658293 CCGCTCCAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.08, C:0.23, G:0.00, T:0.69
Consensus pattern (21 bp):
TTATTATTCCTTTCCCTTTTC
Found at i:4661941 original size:2 final size:2
Alignment explanation
Indices: 4661934--4661961 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4661924 ATTTTACATT
4661934 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4661962 AAGAGGATCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4667564 original size:20 final size:20
Alignment explanation
Indices: 4667539--4667583 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
4667529 CAAAGAAGAT
*
4667539 TACTTCTCAGCATTCAAATA
1 TACTTCTCAGCATTCAAAAA
4667559 TACTTCTCAGCATTCAAAAA
1 TACTTCTCAGCATTCAAAAA
4667579 TACTT
1 TACTT
4667584 TTAAATAGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.36, C:0.24, G:0.04, T:0.36
Consensus pattern (20 bp):
TACTTCTCAGCATTCAAAAA
Found at i:4670102 original size:19 final size:19
Alignment explanation
Indices: 4669995--4670103 Score: 62
Period size: 19 Copynumber: 5.5 Consensus size: 19
4669985 AATACAACAT
* *
4669995 AATT-TATATAATATTTTAA
1 AATTATATATAATAATAT-A
*
4670014 AATTATATATTAAT-ATATT
1 AATTATATA-TAATAATATA
* * *
4670033 ATTTATATTTTATAATATA
1 AATTATATATAATAATATA
*
4670052 TAATGTATAATATAAATAATAAA
1 -AAT-TAT-ATAT-AATAATATA
*
4670075 GAACT-TATATAATAATATA
1 -AATTATATATAATAATATA
4670094 AATTATATAT
1 AATTATATAT
4670104 TTTAATAGTT
Statistics
Matches: 67, Mismatches: 15, Indels: 16
0.68 0.15 0.16
Matches are distributed among these distances:
18 6 0.09
19 28 0.42
20 12 0.18
21 8 0.12
22 4 0.06
23 9 0.13
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.47
Consensus pattern (19 bp):
AATTATATATAATAATATA
Found at i:4670505 original size:21 final size:21
Alignment explanation
Indices: 4670466--4670505 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
4670456 AAATAGTAAT
*
4670466 AATAATTTTTATACTATTTAA
1 AATAATTTTTATACAATTTAA
4670487 AATAATATTTTA-ACAATTT
1 AATAAT-TTTTATACAATTT
4670506 TTATTCCCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (21 bp):
AATAATTTTTATACAATTTAA
Found at i:4674540 original size:38 final size:38
Alignment explanation
Indices: 4674489--4674571 Score: 148
Period size: 38 Copynumber: 2.2 Consensus size: 38
4674479 CAGTTATTGC
*
4674489 GTAGTTTCAATTTGGATGAAGAATTAGGTAATGCAGAT
1 GTAGTTTCAATTTGGATGAAGAATTAGGTAATGCAAAT
4674527 GTAGTTTCAATTTGGATGAAGAATTAGGTAATGCAAAT
1 GTAGTTTCAATTTGGATGAAGAATTAGGTAATGCAAAT
*
4674565 TTAGTTT
1 GTAGTTT
4674572 ATCGGTTGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
38 43 1.00
ACGTcount: A:0.34, C:0.05, G:0.24, T:0.37
Consensus pattern (38 bp):
GTAGTTTCAATTTGGATGAAGAATTAGGTAATGCAAAT
Found at i:4675608 original size:3 final size:3
Alignment explanation
Indices: 4675600--4675654 Score: 85
Period size: 3 Copynumber: 18.7 Consensus size: 3
4675590 TTTGTTGATA
* *
4675600 TAT TAT TAT TAT TAT TAT TAT TAT TGT TAT TGT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
4675648 TA- TAT TA
1 TAT TAT TA
4675655 AACTTGTAGT
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
2 2 0.04
3 45 0.96
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:4679895 original size:22 final size:25
Alignment explanation
Indices: 4679869--4679918 Score: 59
Period size: 23 Copynumber: 2.1 Consensus size: 25
4679859 AAAAAAAATA
*
4679869 AAAAAATTAAA-ATAATAT-AATTT
1 AAAATATTAAATATAATATAAATTT
* *
4679892 AAAATTTTAAATATTATATAAATTT
1 AAAATATTAAATATAATATAAATTT
4679917 AA
1 AA
4679919 TAAAAATTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 9 0.41
24 6 0.27
25 7 0.32
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (25 bp):
AAAATATTAAATATAATATAAATTT
Found at i:4681790 original size:14 final size:13
Alignment explanation
Indices: 4681769--4681810 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
4681759 AGAAATGAGT
4681769 AAAT-AAAAATTA
1 AAATGAAAAATTA
4681781 AAATGAAAAATTA
1 AAATGAAAAATTA
*
4681794 AAATTAATAAATTA
1 AAATGAA-AAATTA
4681808 AAA
1 AAA
4681811 GATCTCATCA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
12 4 0.15
13 14 0.52
14 9 0.33
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.26
Consensus pattern (13 bp):
AAATGAAAAATTA
Found at i:4687347 original size:13 final size:12
Alignment explanation
Indices: 4687325--4687357 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
4687315 TTTTTTGAGG
4687325 TTTTAAAAAAAA
1 TTTTAAAAAAAA
*
4687337 TTTTGAAAAAAA
1 TTTTAAAAAAAA
4687349 -TTTAAAAAA
1 TTTTAAAAAA
4687358 TTCCTAGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (12 bp):
TTTTAAAAAAAA
Found at i:4687983 original size:3 final size:3
Alignment explanation
Indices: 4687975--4688009 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
4687965 AGAAATTTAA
4687975 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
4688010 ATAAATAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:4691548 original size:16 final size:16
Alignment explanation
Indices: 4691527--4691557 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4691517 GTTATTTATA
4691527 GGCTTCTTAAAAGTTG
1 GGCTTCTTAAAAGTTG
*
4691543 GGCTTCTTCAAAGTT
1 GGCTTCTTAAAAGTT
4691558 TATTGTTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.16, G:0.23, T:0.39
Consensus pattern (16 bp):
GGCTTCTTAAAAGTTG
Found at i:4692991 original size:28 final size:26
Alignment explanation
Indices: 4692958--4693026 Score: 75
Period size: 28 Copynumber: 2.5 Consensus size: 26
4692948 AAATAGATAT
* *
4692958 TTTAAAAAATATTGATAAATTTTTTAA
1 TTTAAAAAATATTGATAAA-ATTTGAA
*
4692985 TATTAAATAAATATCGATAAAATTTGAA
1 T-TTAAA-AAATATTGATAAAATTTGAA
4693013 TTATAAAAAATATT
1 TT-TAAAAAATATT
4693027 TTTAATAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
27 8 0.23
28 15 0.43
29 12 0.34
ACGTcount: A:0.52, C:0.01, G:0.04, T:0.42
Consensus pattern (26 bp):
TTTAAAAAATATTGATAAAATTTGAA
Found at i:4696694 original size:84 final size:84
Alignment explanation
Indices: 4696547--4696715 Score: 302
Period size: 84 Copynumber: 2.0 Consensus size: 84
4696537 AGCCCAACAA
* * *
4696547 GATGCAACAAATAACTCTTAGGAAGTTTTGAAGGACTTATCTCTGCCTGTCACTACCGAGGTGGG
1 GATGCAACAAAGAACTCTTAGGAAGTTTTGAAGGACTTATCTCTGCCTGTCACCACCCAGGTGGG
4696612 CCTGTTTTCTTTCGGACAG
66 CCTGTTTTCTTTCGGACAG
*
4696631 GATGCAACAAAGAACTCTTAGGAAGTTTTGAAGGACTTATCTCTGCCTGTCACCACCCTGGTGGG
1 GATGCAACAAAGAACTCTTAGGAAGTTTTGAAGGACTTATCTCTGCCTGTCACCACCCAGGTGGG
4696696 CCTGTTTTCTTTCGGACAG
66 CCTGTTTTCTTTCGGACAG
4696715 G
1 G
4696716 TCCTTTTCTA
Statistics
Matches: 81, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
84 81 1.00
ACGTcount: A:0.23, C:0.22, G:0.24, T:0.30
Consensus pattern (84 bp):
GATGCAACAAAGAACTCTTAGGAAGTTTTGAAGGACTTATCTCTGCCTGTCACCACCCAGGTGGG
CCTGTTTTCTTTCGGACAG
Found at i:4698884 original size:11 final size:11
Alignment explanation
Indices: 4698864--4698905 Score: 66
Period size: 11 Copynumber: 3.8 Consensus size: 11
4698854 AGTAATATCT
4698864 AACAAATCTCA
1 AACAAATCTCA
* *
4698875 AACAAGTCTCT
1 AACAAATCTCA
4698886 AACAAATCTCA
1 AACAAATCTCA
4698897 AACAAATCT
1 AACAAATCT
4698906 GTTATGGGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.50, C:0.26, G:0.02, T:0.21
Consensus pattern (11 bp):
AACAAATCTCA
Found at i:4701225 original size:29 final size:30
Alignment explanation
Indices: 4701183--4701259 Score: 95
Period size: 29 Copynumber: 2.6 Consensus size: 30
4701173 TAATAATCAT
*
4701183 TTAAATTATTAATATTTTATTAT-AATTAA
1 TTAAATTTTTAATATTTTATTATAAATTAA
*
4701212 -TAAATTTTTGAATATTTTATTTTAAATTAA
1 TTAAATTTTT-AATATTTTATTATAAATTAA
*
4701242 TTAAATATTTAAATATTT
1 TTAAAT-TTTTAATATTT
4701260 ATTTTCGTCT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
28 8 0.20
29 12 0.29
30 6 0.15
31 12 0.29
32 3 0.07
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (30 bp):
TTAAATTTTTAATATTTTATTATAAATTAA
Found at i:4701242 original size:30 final size:29
Alignment explanation
Indices: 4701183--4701264 Score: 96
Period size: 30 Copynumber: 2.8 Consensus size: 29
4701173 TAATAATCAT
* *
4701183 TTAAATTATTAATATTTTATTATAATTAA
1 TTAAATTTTTAATATTTTATTTTAATTAA
4701212 -TAAATTTTTGAATATTTTATTTTAAATTAA
1 TTAAATTTTT-AATATTTTATTTT-AATTAA
*
4701242 TTAAATATTTAA-ATATTTATTTT
1 TTAAATTTTTAATAT-TTTATTTT
4701265 CGTCTCATTT
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
28 8 0.17
29 14 0.30
30 16 0.35
31 8 0.17
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (29 bp):
TTAAATTTTTAATATTTTATTTTAATTAA
Found at i:4705577 original size:11 final size:11
Alignment explanation
Indices: 4705537--4705578 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
4705527 AAAATTTTAA
*
4705537 TTATATTGTTT
1 TTATATTATTT
*
4705548 TTAT-GTATTTT
1 TTATATTA-TTT
4705559 TTATATTATTT
1 TTATATTATTT
4705570 TTATATTAT
1 TTATATTAT
4705579 ATCTAAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
10 1 0.04
11 23 0.88
12 2 0.08
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (11 bp):
TTATATTATTT
Found at i:4706998 original size:31 final size:30
Alignment explanation
Indices: 4706953--4707015 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
4706943 AAAGAGATTT
4706953 TTTTTTAAATTTAAAGTCTAAA-TTTAATTAA
1 TTTTTTAAATTTAAA-TCTAAATTTTAA-TAA
*
4706984 TTTTTTATAA-TTAAATTTAAATTTTAATAA
1 TTTTTTA-AATTTAAATCTAAATTTTAATAA
4707014 TT
1 TT
4707016 AAAATTAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
30 10 0.34
31 17 0.59
32 2 0.07
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (30 bp):
TTTTTTAAATTTAAATCTAAATTTTAATAA
Found at i:4707008 original size:21 final size:20
Alignment explanation
Indices: 4706978--4707024 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
4706968 GTCTAAATTT
* *
4706978 AATTAATTTTTTATAATTAA
1 AATTAAATTTTAATAATTAA
*
4706998 ATTTAAATTTTAATAATTAA
1 AATTAAATTTTAATAATTAA
4707018 AATTAAA
1 AATTAAA
4707025 AGTTTAAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AATTAAATTTTAATAATTAA
Found at i:4707035 original size:20 final size:19
Alignment explanation
Indices: 4706987--4707035 Score: 53
Period size: 21 Copynumber: 2.5 Consensus size: 19
4706977 TAATTAATTT
* * *
4706987 TTTATAATTAAATTTAAAT
1 TTTAAAATTAAATTAAAAG
4707006 TTTAATAATTAAAATTAAAAG
1 TTTAA-AATT-AAATTAAAAG
4707027 TTTAAAATT
1 TTTAAAATT
4707036 TTATCAATAG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 4 0.16
20 8 0.32
21 13 0.52
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (19 bp):
TTTAAAATTAAATTAAAAG
Found at i:4709130 original size:40 final size:41
Alignment explanation
Indices: 4709086--4709167 Score: 139
Period size: 40 Copynumber: 2.0 Consensus size: 41
4709076 AGGCATTTGC
4709086 AGGGAGACAGAGTTTATGCTTTTTGC-CTTTGTCAGTTGTG
1 AGGGAGACAGAGTTTATGCTTTTTGCACTTTGTCAGTTGTG
* *
4709126 AGGGAGACAGAGTTTGTGCTTTTTGCATTTTGTCAGTTGTG
1 AGGGAGACAGAGTTTATGCTTTTTGCACTTTGTCAGTTGTG
4709167 A
1 A
4709168 TTTTGAATTG
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
40 25 0.64
41 14 0.36
ACGTcount: A:0.18, C:0.11, G:0.30, T:0.40
Consensus pattern (41 bp):
AGGGAGACAGAGTTTATGCTTTTTGCACTTTGTCAGTTGTG
Found at i:4710247 original size:38 final size:39
Alignment explanation
Indices: 4710202--4710278 Score: 120
Period size: 39 Copynumber: 2.0 Consensus size: 39
4710192 TTAATTTTGA
*
4710202 AAATTTTAAA-TTTCGATATGTTATTAAGAATTAAATGT
1 AAATTTTAAATTTTCGATATGTTACTAAGAATTAAATGT
* *
4710240 AAATTTTAAATTTTTGATATGTTGCTAAGAATTAAATGT
1 AAATTTTAAATTTTCGATATGTTACTAAGAATTAAATGT
4710279 TTAAGGAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
38 10 0.29
39 25 0.71
ACGTcount: A:0.40, C:0.03, G:0.12, T:0.45
Consensus pattern (39 bp):
AAATTTTAAATTTTCGATATGTTACTAAGAATTAAATGT
Found at i:4711716 original size:208 final size:208
Alignment explanation
Indices: 4711241--4711774 Score: 688
Period size: 208 Copynumber: 2.6 Consensus size: 208
4711231 TCAATAATAA
* * * *
4711241 CAACAACAACAACAACTCTAACAAAAATACATAGCC-ATTTGTCAAAATCTTAAAATTTTCTTTG
1 CAACAACAACAAGAATTCCAACAAAAATACATA-CCTATTTGTCAAAATCTTAAATTTTTCTTTG
** * *
4711305 TAAAAGAAGAAAGAAAAGAAAAAAGTTCAAATTTTCTTGTTGATTTGTGAGCTTTTCTAATCTAG
65 TAAAAGAA-AAAGAAAAGAAAAAAGTTTGAATTTTCTTGTTGATTTGTGAGCTTTTTTAATATAG
* * * * *
4711370 GTCGATGGTGGAATCAGAAAATAATAAGACAAAATCATCATCTAGTTCGATGTTCTTCAATCAAT
129 ATCGATGGTGGAATCAGAAAATAACAAGACAAAATCATCATCTAGTTCGATATTCTTCAATAAAA
*
4711435 AATCATTATCATCAT
194 AATCATCATCATCAT
*
4711450 CAACAACAACAAGAATTCCAACAAAAATACATACCTATTTGTCAAAATCTTGAATTTTTCTTTGT
1 CAACAACAACAAGAATTCCAACAAAAATACATACCTATTTGTCAAAATCTTAAATTTTTCTTTGT
* * *
4711515 AAAAGAAAAAGAAAAGAAAAAAGTTTGAATTTTTTTGTTGATTTGTGAGTTTTTTTTATATAGAT
66 AAAAGAAAAAGAAAAGAAAAAAGTTTGAATTTTCTTGTTGATTTGTGAGCTTTTTTAATATAGAT
* * * **
4711580 CGATGGCT-GAATTAGGAAATTACAAGACAAAATCA-CATCTAGGTT-GATATTCTTTGATAAAA
131 CGATGG-TGGAATCAGAAAATAACAAGACAAAATCATCATCTA-GTTCGATATTCTTCAATAAAA
* *
4711642 AATTATCATCATTAT
194 AATCATCATCATCAT
* * * * *
4711657 CAATAACAACAAGAATTCCAACAAAAACACATATCTATTTTGTTAAAATATTAAATTTTTCTTTG
1 CAACAACAACAAGAATTCCAACAAAAATACATACCTA-TTTGTCAAAATCTTAAATTTTTCTTTG
*
4711722 TAAAAG---AA-AAAAGAAAAAATTTTGAATTTTCTTGTTGATTTGTGAGCTTTTTT
65 TAAAAGAAAAAGAAAAGAAAAAAGTTTGAATTTTCTTGTTGATTTGTGAGCTTTTTT
4711775 GATCTGGGTC
Statistics
Matches: 287, Mismatches: 34, Indels: 13
0.86 0.10 0.04
Matches are distributed among these distances:
204 42 0.15
205 2 0.01
207 64 0.22
208 114 0.40
209 65 0.23
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.34
Consensus pattern (208 bp):
CAACAACAACAAGAATTCCAACAAAAATACATACCTATTTGTCAAAATCTTAAATTTTTCTTTGT
AAAAGAAAAAGAAAAGAAAAAAGTTTGAATTTTCTTGTTGATTTGTGAGCTTTTTTAATATAGAT
CGATGGTGGAATCAGAAAATAACAAGACAAAATCATCATCTAGTTCGATATTCTTCAATAAAAAA
TCATCATCATCAT
Found at i:4711928 original size:23 final size:22
Alignment explanation
Indices: 4711885--4711940 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
4711875 CACATACGCA
*
4711885 TTTGTCAAAATCTTGAATTTTTC
1 TTTG-CAAAATATTGAATTTTTC
4711908 TTTGCAAAATATTGAATTTTTC
1 TTTGCAAAATATTGAATTTTTC
4711930 TTTGCAAAATA
1 TTTGCAAAATA
4711941 AGGAAAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 28 0.88
23 4 0.12
ACGTcount: A:0.32, C:0.11, G:0.09, T:0.48
Consensus pattern (22 bp):
TTTGCAAAATATTGAATTTTTC
Found at i:4718012 original size:16 final size:16
Alignment explanation
Indices: 4717991--4718021 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4717981 ATTATTGAAT
4717991 AATATTTTTTAAAATA
1 AATATTTTTTAAAATA
*
4718007 AATATTTTTTGAAAT
1 AATATTTTTTAAAAT
4718022 CTTTAAGACG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (16 bp):
AATATTTTTTAAAATA
Found at i:4718402 original size:19 final size:19
Alignment explanation
Indices: 4718360--4718396 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
4718350 TGAATAATAC
4718360 AAATAACACTGAGATACAT
1 AAATAACACTGAGATACAT
* *
4718379 AAATAACATTGATATACA
1 AAATAACACTGAGATACA
4718397 ACAATATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.54, C:0.14, G:0.08, T:0.24
Consensus pattern (19 bp):
AAATAACACTGAGATACAT
Found at i:4719434 original size:22 final size:23
Alignment explanation
Indices: 4719409--4719451 Score: 79
Period size: 22 Copynumber: 1.9 Consensus size: 23
4719399 ACATATATTC
4719409 TTATCATTATAA-ATGTTATTTA
1 TTATCATTATAATATGTTATTTA
4719431 TTATCATTATAATATGTTATT
1 TTATCATTATAATATGTTATT
4719452 GTATATTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.56
Consensus pattern (23 bp):
TTATCATTATAATATGTTATTTA
Found at i:4721484 original size:20 final size:20
Alignment explanation
Indices: 4721461--4721513 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
4721451 AAATTTTTTT
**
4721461 AATTTTTAAAATACTTTTAA
1 AATTTTTAAAATAAATTTAA
*
4721481 AATTTTTAAAAAAAATTTAA
1 AATTTTTAAAATAAATTTAA
4721501 AATTTTTTAAAAT
1 AA-TTTTTAAAAT
4721514 TTATTTTTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 19 0.68
21 9 0.32
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (20 bp):
AATTTTTAAAATAAATTTAA
Found at i:4721486 original size:8 final size:9
Alignment explanation
Indices: 4721448--4721515 Score: 55
Period size: 9 Copynumber: 7.0 Consensus size: 9
4721438 TTAGAAAATC
4721448 TTAAAATTT
1 TTAAAATTT
**
4721457 TTTTAATTT
1 TTAAAATTT
4721466 TTAAAATACTT
1 TTAAAAT--TT
4721477 TTAAAATTT
1 TTAAAATTT
**
4721486 TTAAAAAAAAT
1 TT--AAAATTT
4721497 TTAAAATTTT
1 TTAAAA-TTT
4721507 TTAAAATTT
1 TTAAAATTT
4721516 ATTTTTATAC
Statistics
Matches: 46, Mismatches: 8, Indels: 10
0.72 0.12 0.16
Matches are distributed among these distances:
9 23 0.50
10 7 0.15
11 16 0.35
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (9 bp):
TTAAAATTT
Found at i:4723072 original size:2 final size:2
Alignment explanation
Indices: 4723067--4723098 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4723057 GTGTGTGTGT
4723067 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
4723099 AGTCTTACTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:4725147 original size:37 final size:37
Alignment explanation
Indices: 4725075--4725148 Score: 114
Period size: 37 Copynumber: 2.0 Consensus size: 37
4725065 AGTAAATCTT
*
4725075 ACTCATTGCAATATCAAGCAACTCAAAAAGGAAACTA
1 ACTCATTGCAATATCAAGCAACTCAAAAAGAAAACTA
*
4725112 ACTCATTGCAATATCAAGCAACTTAAAATA-AAAACTA
1 ACTCATTGCAATATCAAGCAACTCAAAA-AGAAAACTA
4725149 TTATAATAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
37 33 0.97
38 1 0.03
ACGTcount: A:0.50, C:0.20, G:0.08, T:0.22
Consensus pattern (37 bp):
ACTCATTGCAATATCAAGCAACTCAAAAAGAAAACTA
Found at i:4727137 original size:21 final size:19
Alignment explanation
Indices: 4727101--4727140 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
4727091 AAAAACAAAA
*
4727101 AATTTGAAAACTAAAGAAG
1 AATTTGAAAAATAAAGAAG
4727120 AATTTAGAAAAATGAAAGAAG
1 AATTT-GAAAAAT-AAAGAAG
4727141 GCGGCTCAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 6 0.33
21 7 0.39
ACGTcount: A:0.60, C:0.03, G:0.17, T:0.20
Consensus pattern (19 bp):
AATTTGAAAAATAAAGAAG
Found at i:4731428 original size:21 final size:21
Alignment explanation
Indices: 4731389--4731428 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
4731379 TACTTCACAA
* **
4731389 ATTTTATTTTTTTTTTAAATT
1 ATTTTATTTTTGTGGTAAATT
4731410 ATTTTATTTTTGTGGTAAA
1 ATTTTATTTTTGTGGTAAA
4731429 CTTTTTAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.25, C:0.00, G:0.07, T:0.68
Consensus pattern (21 bp):
ATTTTATTTTTGTGGTAAATT
Found at i:4734741 original size:30 final size:30
Alignment explanation
Indices: 4734705--4734764 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
4734695 GTGTCATTAG
*
4734705 TTAGCTTAGAGTTTTGAGTGTAATTAGAGA
1 TTAGCTTAGAGTTTTGAGTGTAATAAGAGA
**
4734735 TTAGCTTATTGTTTTGAGTGTAATAAGAGA
1 TTAGCTTAGAGTTTTGAGTGTAATAAGAGA
4734765 ATAGAGGTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.03, G:0.25, T:0.42
Consensus pattern (30 bp):
TTAGCTTAGAGTTTTGAGTGTAATAAGAGA
Found at i:4735958 original size:3 final size:3
Alignment explanation
Indices: 4735950--4735980 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
4735940 TTGAAACATC
*
4735950 TTA TTA TTA TTA TTA TTG TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
4735981 CTTGGATACA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:4742584 original size:30 final size:30
Alignment explanation
Indices: 4742550--4742607 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
4742540 TAGGTGACTG
** *
4742550 ATAAATAATTTTTTAAATATTATATTAATA
1 ATAAATAATAATTTAAATATTACATTAATA
*
4742580 ATAAATTATAATTTAAATATTACATTAA
1 ATAAATAATAATTTAAATATTACATTAA
4742608 AAATTTTTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (30 bp):
ATAAATAATAATTTAAATATTACATTAATA
Found at i:4751354 original size:22 final size:22
Alignment explanation
Indices: 4751325--4751368 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
4751315 AATACATGAA
**
4751325 ATATAATTTTTTAAA-AAAATT
1 ATATAATTAATTAAACAAAATT
4751346 ATATGAATTAATTAAACAAAATT
1 ATAT-AATTAATTAAACAAAATT
4751369 TCAAGCTCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 4 0.21
22 9 0.47
23 6 0.32
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (22 bp):
ATATAATTAATTAAACAAAATT
Found at i:4762097 original size:10 final size:10
Alignment explanation
Indices: 4762074--4762102 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
4762064 ATTTTATTAG
4762074 TTAAAATA-A
1 TTAAAATATA
4762083 TTAAAATATA
1 TTAAAATATA
4762093 TTAAAATATA
1 TTAAAATATA
4762103 AAAATTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 8 0.42
10 11 0.58
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
TTAAAATATA
Found at i:4762710 original size:123 final size:124
Alignment explanation
Indices: 4762577--4762808 Score: 387
Period size: 124 Copynumber: 1.9 Consensus size: 124
4762567 GTTTGTTCTT
*
4762577 TGGACCTACACCAA-TTGGAAAAATAGTGTAAAGCAACGAGTTGT-CTGCATTTTTCCGTCCAAT
1 TGGACCTACACCAATTTGGAAAAATAGTGTAAAGCAACGAGTTATGC-GCATTTTTCCGTCCAAT
*
4762640 CTCATAGACAATTCACTCCTGCTGTTATCCATTTCCACACCCATTTACACGTTTGCTCCC
65 CTCATAGACAATTCACTCCTGCTGTCATCCATTTCCACACCCATTTACACGTTTGCTCCC
* * *
4762700 TGGACCTACACCAATTTGGAAAATTAGTGTTAAGCAACGAGTTATGCGCATTTTTCCGTCTAATC
1 TGGACCTACACCAATTTGGAAAAATAGTGTAAAGCAACGAGTTATGCGCATTTTTCCGTCCAATC
*
4762765 TCATAGACAATTGACTCCTGCTGTCATCCATTTCCACACCCATT
66 TCATAGACAATTCACTCCTGCTGTCATCCATTTCCACACCCATT
4762809 GACATGTGTG
Statistics
Matches: 101, Mismatches: 6, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
123 14 0.14
124 86 0.85
125 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.31
Consensus pattern (124 bp):
TGGACCTACACCAATTTGGAAAAATAGTGTAAAGCAACGAGTTATGCGCATTTTTCCGTCCAATC
TCATAGACAATTCACTCCTGCTGTCATCCATTTCCACACCCATTTACACGTTTGCTCCC
Found at i:4762828 original size:124 final size:123
Alignment explanation
Indices: 4762534--4762831 Score: 386
Period size: 124 Copynumber: 2.4 Consensus size: 123
4762524 AAATTGGCTC
* * * * **
4762534 CTCCTG-TGTCATCCTTTTACACA-CCGTTGGCAAGTTTGTTCTTTGGACCTACACCAATTGGAA
1 CTCCTGCTGTCATCCATTTCCACACCCATTGACAAGTTTGTTCCATGGACCTACACCAATTGGAA
*
4762597 AAATAGTGTAAAGCAACGAGTTGTCTGCATTTTTCCGTCCAATCTCATAGACAATTCA
66 AAATAGTGTAAAGCAACGAGTTATCTGCATTTTTCCGTCCAATCTCATAGACAATTCA
* * * * *
4762655 CTCCTGCTGTTATCCATTTCCACACCCATTTACACGTTTGCTCCCTGGACCTACACCAATTTGGA
1 CTCCTGCTGTCATCCATTTCCACACCCATTGACAAGTTTGTTCCATGGACCTACACCAA-TTGGA
* * * *
4762720 AAATTAGTGTTAAGCAACGAGTTATGC-GCATTTTTCCGTCTAATCTCATAGACAATTGA
65 AAAATAGTGTAAAGCAACGAGTTAT-CTGCATTTTTCCGTCCAATCTCATAGACAATTCA
* * *
4762779 CTCCTGCTGTCATCCATTTCCACACCCATTGACATGTGTGTTCGATGGACCTA
1 CTCCTGCTGTCATCCATTTCCACACCCATTGACAAGTTTGTTCCATGGACCTA
4762832 GACCTAACCC
Statistics
Matches: 151, Mismatches: 22, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
121 6 0.04
122 14 0.09
123 27 0.18
124 103 0.68
125 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.16, T:0.33
Consensus pattern (123 bp):
CTCCTGCTGTCATCCATTTCCACACCCATTGACAAGTTTGTTCCATGGACCTACACCAATTGGAA
AAATAGTGTAAAGCAACGAGTTATCTGCATTTTTCCGTCCAATCTCATAGACAATTCA
Found at i:4763106 original size:27 final size:27
Alignment explanation
Indices: 4763057--4763120 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
4763047 TATATTGTAT
* *
4763057 ATAAAATTAT-AATGAGATAAAATAAA
1 ATAATATTATAAATAAGATAAAATAAA
* * *
4763083 ATGATATTATAAATAAGATTAAATTAA
1 ATAATATTATAAATAAGATAAAATAAA
4763110 ATAATATTATA
1 ATAATATTATA
4763121 TTATTTTTAT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
26 8 0.26
27 23 0.74
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.34
Consensus pattern (27 bp):
ATAATATTATAAATAAGATAAAATAAA
Found at i:4763441 original size:20 final size:19
Alignment explanation
Indices: 4763406--4763449 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
4763396 TCTATTTATC
4763406 ATTTTATGTACTAAATATA
1 ATTTTATGTACTAAATATA
4763425 ATTTTAATGTA-TAAA-ATA
1 ATTTT-ATGTACTAAATATA
4763443 ATCTTTA
1 AT-TTTA
4763450 CAACTACAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
18 6 0.26
19 12 0.52
20 5 0.22
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.48
Consensus pattern (19 bp):
ATTTTATGTACTAAATATA
Done.